Good afternoon,

I am trying to read a maf file with a clinical data file (from TCGA) via

maf <- read.maf(maf = maf_file, clinicalData = clinical_data)

The issue is that in the clinical data file the tumor sample barcode name is short (12 character, e.g.
TCGA-3L-AA1B), while in the maf file the tumor sample barcode name is much longer (e.g. TCGA-3L-AA1B-01A-11D-A36X-10).

I tried to modify the tumor sample barcode via

maf@data$Tumor_Sample_Barcode<-substr(maf@data$Tumor_Sample_Barcode,1,12)

However, this only modifies the name in maf@data, but the tumor sample barcode can also be found e.g. in maf@variants.per.sample or maf@variant.type.summary. And this way it is only updated in maf@data.

Any idea?

Thanks so much!!